The neuropeptide Y receptor gene repository, phylogeny and comparative expression in allotetraploid common carp.

NPY-family receptors belong to G protein-coupled receptors (GPCR), which lays a physiological foundation for the transmembrane transport of an endogenous appetite-stimulating factor neuropeptide Y and related peptides. In this study, we investigated the npyr genes in ten representative species, and twelve npyr genes were identified from allotetraploid C. carpio, the npyr gene number of C. carpio was twice the number of its subgenome B progenitor-like diploid Poropuntius huangchuchieni. Phylogenetic analysis showed that all npyr genes were divided into three subgroups, and they underwent strong purifying selection according to selection pressure analysis. Subsequently, synteny analysis showed that most npyr genes were evenly distributed on the homologous chromosomes of two subgenomes in allotetraploid C. carpio, in which npy1r and npy2r were tandem duplicated, respectively. In addition, the global expression of npyr genes during embryonic development in allotetraploid C. carpio suggested the potential function of npyr genes in immunity and reproduction. In adult tissues, npyr genes were mainly distributed in the brain, gonad, and skin, which displayed a similar expression pattern between the C. carpio B subgenome and P. huangchuchieni. In general, our research could provide reference information for future exploration of the NPY receptors and neuroendocrine system of allotetraploid C. carpio and vertebrates.

Genome-wide mining of gpx gene family provides new insights into cadmium stress responses in common carp (Cyprinus carpio).

Glutathione peroxidase (Gpx) is an important member of antioxidant enzymes, which can play a vital role in metabolizing reactive oxygen species (ROS) and in maintaining cell homeostasis. In order to study the evolutionary dynamics of gpx gene family in allotetraploid fish species, we identified a total of 14 gpx genes in common carp Cyprinus carpio, while 9 gpx genes were discovered in the diploid progenitor-like species Poropuntius huangchuchieni. Comparative genomic analysis and phylogenetic analysis revealed that the common carp gpx genes had significant expansion and were divided into five distinct subclades. Exon-intron distribution patterns and conserved motif analysis revealed highly conserved evolutionary patterns. Transcript profiles suggested that different gpx genes had specific patterns of regulation during early embryonic development. In adult tissues, gpx genes had a relatively broad expression distribution, most of which were highly expressed in the gills, intestines, and gonads. RT-qPCR studies showed that most gpx genes were downregulated during the initial cd2+ treatment stage. Dietary supplementation of Bacillus coagulans at different concentrations (Group 2 of 1.0 × 107 cfu/g, Group 3 of 1.0 × 108 cfu/g, and Group 4 of 1.0 × 109 cfu/g) induced different regulatory responses of gpx subclades. This result suggested that the appropriate concentration of B. coagulans can improve gpx gene expression when exposed to heavy metal cadmium treatment, which may play a vital role in the resistance to oxidative stress and immune responses. This study has expanded our understanding of the functional evolution of the gpx gene family in common carp.

Chromosome assembly of Collichthys lucidus, a fish of Sciaenidae with a multiple sex chromosome system.

Collichthys lucidus (C. lucidus) is a commercially important marine fish species distributed in coastal regions of East Asia with the X1X1X2X2/X1X2Y multiple sex chromosome system. The karyotype for female C. lucidus is 2n = 48, while 2n = 47 for male ones. Therefore, C. lucidus is also an excellent model to investigate teleost sex-determination and sex chromosome evolution. We reported the first chromosome genome assembly of C. lucidus using Illumina short-read, PacBio long-read sequencing and Hi-C technology. An 877 Mb genome was obtained with a contig and scaffold N50 of 1.1 Mb and 35.9 Mb, respectively. More than 97% BUSCOs genes were identified in the C. lucidus genome and 28,602 genes were annotated. We identified potential sex-determination genes along chromosomes and found that the chromosome 1 might be involved in the formation of Y specific metacentric chromosome. The first C. lucidus chromosome-level reference genome lays a solid foundation for the following population genetics study, functional gene mapping of important economic traits, sex-determination and sex chromosome evolution studies for Sciaenidae and teleosts.

Surface Modification of Poly(dimethylsiloxane) Using Ionic Complementary Peptides to Minimize Nonspecific Protein Adsorption.

Poly(dimethylsiloxane) (PDMS) has become a widely used material for microfluidic and biological applications. However, PDMS has unacceptably high levels of nonspecific protein adsorption, which significantly lowers the performance of PDMS-based microfluidic chips. Most existing methods to reduce protein fouling of PDMS are to make the surface more hydrophilic by surface oxidization, polymer grafting, and physisorbed coatings. These methods suffer from the relatively short-term stability, the multistep complex treatment procedure, or the insufficient adsorption reduction. Herein, we developed a novel and facile modification method based on self-assembled peptides with well-tailored amino acid composition and sequence, which can also interact strongly with the PDMS surface in the same way as proteins, for suppressing the nonspecific protein fouling and improving the biocompatibility of PDMS-based microfluidic chips. We first demonstrated that an ionic complementary peptide, EAR16-II with a sequence of [(Ala-Glu-Ala-Glu-Ala-Arg-Ala-Arg)2], can readily self-assemble into an amphipathic film predominantly composed of tightly packed ß-sheets on the native hydrophobic and plasma-oxidized hydrophilic PDMS surfaces upon low concentrations of carbohydrates. The self-assembled EAR16-II amphipathic film exposed its hydrophobic side to the solution and thus rendered the PDMS surface hydrophobic with water contact angles (WCAs) of around 110.0°. However, the self-assembled EAR16-II amphipathic film exhibited excellent protein-repelling and blood compatibility properties comparable to or better than those obtained with previously reported methods. A schematic model has been proposed to explain the interactions of EAR16-II with the PDMS surface and the antifouling capability of EAR16-II coatings at a molecular level. The current work will pave the way to the development of novel coating materials to address the nonspecific protein adsorption on PDMS, thereby broadening the potential uses of PDMS-based microfluidic chips in complex biological analysis.